UBChttps://ubc.uu.nl
Utrecht Bioinformatics CenterTue, 16 Apr 2019 13:08:30 +0000en-US
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1 https://ubc.uu.nl/wp-content/uploads/2017/11/cropped-Asset-1-32x32.pngUBChttps://ubc.uu.nl
3232National e-learning platform for Bioinformaticshttps://ubc.uu.nl/national-e-learning-platform-for-bioinformatics/
Mon, 15 Apr 2019 14:26:24 +0000https://ubc.uu.nl/?p=2323The Utrecht Bioinformatics Center and BioSB join forces to develop and offer interesting bioinformatics and systems biology courses that can be followed within the comforts of your own home or work environment. At the moment the UBC already runs her e-learning platform for most of...

]]>The Utrecht Bioinformatics Center and BioSB join forces to develop and offer interesting bioinformatics and systems biology courses that can be followed within the comforts of your own home or work environment.

At the moment the UBC already runs her e-learning platform for most of the UBC related bioinformatics courses. The courses offered here are a combined effort of our UBC community and make a great starting point for a national e-learning platform. Bas van Breukelen, our UBC Education coordinator, will be a member in the BioSB educational committee.

The joint platform will run on the well know Moodle e-learning platform which is an open source, SCORM compatible and flexible platform.

Are you interested in developing and offering your e-learning course via this platform?Please, get in touch with Bas van Breukelen for more information.

]]>With three renowned keynote speakers, Mustafa Kammash, Michal Linial and Eran Segal talking about control theory, evolution of translational control and personalized treatment using microbiome data, the BioSB conference provided a glimpse on international developments in bioinformatics and systems biology.

With over twenty posters, eight selected and invited talks and the best BioSB2019 poster prize for Jayne Hehir-Kwa, the research groups from Utrecht Bioinformatics Center had a strong and clear presence at the BioSB2019 conference.

Breakout session on Education

Adrien Melquiond at BioSB2019

In the Education breakout session Adrien Melquiond shared the UBC vision on teaching and the challenge of data processing in Life Sciences. To us, the only sustainable solution is that every life scientist also becomes a data scientist, capable of handling the entire data life cycle, from experiments to processing and extraction of signal, and finally their analysis. To overcome current bottlenecks we need tailored solutions and year-round support from local experts in the field. Adrien presented the computing resources UBC is using and a short demo. This set-up raised a lot of interest from our ELIXIR partners and triggered rich discussions with other Universities that are facing similar challenges.

Translational bioinformatics

The PhD retreat had translational bioinformatics as a theme and featured dr. Anna-Lena Lamprecht and dr. Alessio Marcozzi as speakers from Utrecht as well as dr. Joana Goncalves from Delft. Preceding the BioSB2019 conference, YoungCB organized this yearly PhD retreat. YoungCB is the organization of PhD students within bioinformatics and/or systems biology.

On the 2nd and 3rd of April, the BioSB conference took place in Lunteren. With over 370 bioinformaticians, system biologists, data scientists and participants from industry, the conference provided a fantastic opportunity to hear about the latest developments at academic institutes in The Netherlands, meet with fellow scientists and hear great bioinformatics and systems biology talks.

BioSB2020

Next year, the BioSB2020 conference will be on April 21-22 and will be organized by Utrecht Bioinformatics Center, so mark your calendar for another great conference.

]]>Sergio’s tips for your conference presentationhttps://ubc.uu.nl/tips-for-your-conference-presentation/
Mon, 15 Apr 2019 08:32:02 +0000https://ubc.uu.nl/?p=2313“Although I did not make it to the finals of the Breaking Science pitching competition, I had a blast during this course. I think it was one of the most useful courses that I followed during my PhD. It has dramatically changed the way I...

“Although I did not make it to the finals of the Breaking Science pitching competition, I had a blast during this course. I think it was one of the most useful courses that I followed during my PhD. It has dramatically changed the way I focus my talks during a conference.”

All Breaking Science competitors had the same training before presenting their complex research to a laymen audience in only three minutes. Sergio gives us his three most important tips of all things he learnt during the training.

Interpretation of the audience

“In my honest opinion scientists always spend a lot of time preparing our slides for a presentation but we rarely practice nor get feedback after a presentation regarding our presentation style. I found it very interesting to hear how my gestures, attention with the audience, tempo are interpreted by my audience. We need to ask for this kind of feedback! This course provided me with exercises to dramatically improve my presentation style.”

Importance of the introduction

“In addition: always modify your presentation based on your target audience. If people get lost or find your presentation boring at the beginning they will not follow you anymore during your talk. Make an introduction in which you emphasize the importance of your subject.”

Change the structure

“To make your presentation stand out from others and make it easy to be remembered, you may change the basic structure of your talk. For instance start with the problem instead of an introduction and share the challenges that you encounter. Just after that, tell about the methods used and end with the solution you found.“

]]>50 years bioinformaticshttps://ubc.uu.nl/introduction-50-years-bioinformatics/
Mon, 15 Apr 2019 08:19:10 +0000https://ubc.uu.nl/?p=2308In 2020, it will be 50 years since Paulien Hogeweg and Ben Hesper first coined the term ‘bioinformatica’. Since bioinformatics is now a mature and thriving research field, indispensable in addressing life science research challenges, we think this occasion should no go by unnoticed. Therefore,...

]]>In 2020, it will be 50 years since Paulien Hogeweg and Ben Hesper first coined the term ‘bioinformatica’. Since bioinformatics is now a mature and thriving research field, indispensable in addressing life science research challenges, we think this occasion should no go by unnoticed.

Paulien Hogeweg

Therefore, to celebrate the genesis of bioinformatics, we will organize a number of activities throughout the year. We will, for example, organize next years BioSB conference and dedicate part of the program to this part of science history.

Ben Hesper

In the original definition bioinformatics was not primarily data analysis. Instead it emphasized the need to study biological systems as information processing phenomena, for example with information accumulation in evolution. In this way, it describes the research line that Paulien Hogeweg is still carrying out in Utrecht nowadays. Interestingly, with the data accumulation in modern-day life sciences, this information processing perspective is becoming more and more relevant.

In addition to inform you on our intentions for next year, we also ask you for hands-on help, input, creative ideas or original propositions to celebrate this momentous occasion. We are still in the process of thinking about how to organise this milestone and attract maximal attention for which all help is welcome

]]>Keynote speakers UBC symposium 2019https://ubc.uu.nl/keynote-speakers-ubc-symposium-2019/
Tue, 09 Apr 2019 14:06:02 +0000https://ubc.uu.nl/?p=2289Theme of this year’s UBC symposium is ‘Bioinformatics 4 Life’ and we are proud to announce two great keynote speakers. Thijs Ettema from Uppsala University (Sweden): Dr. Ettema’s lab is focused on characterizing microbial diversity using state-of-the-art technologies such as single-cell sequencing and metagenomics. By assessing...

]]>Theme of this year’s UBC symposium is ‘Bioinformatics 4 Life’ and we are proud to announce two great keynote speakers.

Thijs Ettema

Thijs Ettema from Uppsala University (Sweden): Dr. Ettema’s lab is focused on characterizing microbial diversity using state-of-the-art technologies such as single-cell sequencing and metagenomics. By assessing microbial diversity, he is also attempting to gain additional insights in evolutionary differences between the main domains of life.

Sara Pulit

Sara Pulit from Vertex Pharmaceuticals, San Diego: Sara has been working in Utrecht, with a strong emphasis on genetic association studies to unravel genetic predispositions for different diseases. She has recently moved to Vertex Pharmaceuticals where she continues to apply genetics and bioinformatics in an industrial setting.

This year will feature our sixth edition of the yearly Utrecht Bioinformatics Center Symposium. Save the date to join a full day of interesting keynotes, local PI’s and selected talks from PhD candidates and postdocs as well as a poster session during lunch.

]]>New Research Data Management serviceshttps://ubc.uu.nl/new-research-data-management-services-utrecht-bioinformatics-center/
Tue, 09 Apr 2019 12:27:35 +0000https://ubc.uu.nl/?p=2284FAIR data? ORCID-ID? Metadata? If these terms raise more questions than answers, maybe it’s time to receive an introduction or counselling session about research data management (RDM). Intro session is now available and bookable A short and sweet presentation is ready for your consumption and...

]]>FAIR data? ORCID-ID? Metadata? If these terms raise more questions than answers, maybe it’s time to receive an introduction or counselling session about research data management (RDM).

Intro session is now available and bookable

A short and sweet presentation is ready for your consumption and can be extended by a topic of choice: whether it is about Data Management Plans (DMP), a short dive into FAIR data-sets, or any other RDM related topic that burns holes into your mind.

An intro sessions exists of 15 minutes of essential presentation and 45 minutes of additional content or hands-on time to revise your current workflow as well. You can book this RDM intro session now with the UBC Data Steward Jasmin Böhmer.

Walk in counselling hours

Starting this month there will be monthly walk in counselling hours for data stewardship and RDM related matters. The first counselling hours will take place at the UMC Utrecht, Stratenum on the Second Floor (STR.2.121), on:

]]>Fully reproducible analysis on cloud architecturehttps://ubc.uu.nl/fully-reproducible-analysis-on-cloud-architecture/
Tue, 12 Feb 2019 09:52:46 +0000https://ubc.uu.nl/?p=2250To make the High Performance Computing facility (HPC) ready for the future we realised new workflows and authentication procedures. These components are crucial to the future of Life Science research, because they allow researchers to develop analysis that are fully reproducible and can also run...

]]>To make the High Performance Computing facility (HPC) ready for the future we realised new workflows and authentication procedures. These components are crucial to the future of Life Science research, because they allow researchers to develop analysis that are fully reproducible and can also run on cloud architectures.

Workflows

Researchers from the Princess Maxima Center have taken the initiative to test a Cromwell setup on the HPC. The positive results of this trial give cause to evaluate whether this set-up is ready for further deployment, or if additional testing is required. A parallel pilot set-up of Arvados integrated with Jupyter notebooks is now complete, and will also be evaluated by users in the coming months.

Authentication

Being able to run analysis on different systems requires users to authenticate across those systems in a uniform and structured manner. The HPC team started a pilot project with SURF on their newly developed Science Collaboration Zone. This system allows Dutch institutes to share their credentials easily and securely for computing resources. Researchers will identify as a unique entity across the entire system, regardless of institute or architecture.

New HPC management

The biggest update from the HPC team is that Joep de Ligt has left us. At the end of January he started work in New Zealand as Head of Bioinformatics at the Institute of Environmental Science and Research. Joep has been instrumental in leading the HPC facility for the past few years, and his contribution has ensured that the HPC is ready for the future. We thank Joep for his great work and wish him all the best for the future.

Ies Nijman has been appointed as our new HPC coordinator, and will of course be supported by the trusty and knowledgeable HPC team.

HPC-user meeting

The HPC community is constantly growing, and we are looking for opportunities to connect the relevant users to these pilot projects so they can give feedback and ideas on the future direction of the HPC. In addition to an HPC-council meeting for PIs, we will also organise a user meeting on Wednesday, 6 March, from 13:00-14:00. Location: UMC Utrecht, Stratenum, Vondelzaal (3.108).

Please join the meeting to get yourself up-to-date about the new possibilities and to help us tune the system to your needs where possible.

]]>Young UBC member Sergio Arredondo-Alonso will explain his research for a general public in just three minutes. After a training on how to best do this, Sergio will present his pitch to the audience and jury.

Sergio is a Bioinformatics PhD candidate at UMC Utrecht, with a background in microbiology and bioinformatics. “My main research interest is in the field of Microbial Genomics and the interplay between antimicrobial resistance genes and plasmids. In this field, I am particularly interested in the development of new tools to predict plasmid sequences from whole-genome sequencing and the emergence of new long-read based technologies.”

The research project in short

Sergio is already trying to give a short and clear explanation of his research. “Antimicrobial resistance is considered as one of the biggest health problems from this century. The increase of antibiotic resistance around the world narrows the number of effective treatments available against bacterial infections. Antimicrobial resistance can easily be spread among bacterial populations through the exchange of plasmid sequences. In our research group, we use the combination of short-read (Illumina NextSeq/Miseq) and long-read technologies (Oxford Nanopore Technologies) to obtain complete genomes from a major nosocomial pathogen (Enterococcus faecium) and study the role of plasmids in the dissemination of vancomycin resistance and host-adaptation. Information derived from the complete genomes was used to develop a new tool called ‘mlplasmids’ in which we trained a support vector machine to classify short-read sequences as plasmid- or chromosome-derived.”

]]>Utrecht Life Science Hubs & Bioinformaticshttps://ubc.uu.nl/utrecht-life-science-hubs-bioinformatics/
Mon, 11 Feb 2019 14:26:37 +0000https://ubc.uu.nl/?p=2256Utrecht University has invested in four different Life Science hubs: the Utrecht Exposome Hub, the Utrecht Platform for Organoid Technology, the Utrecht Molecular Immunology Hub and the Utrecht Advanced In Vitro Models Hub. What role do bioinformaticians play in the ULS hubs? These hubs bring...

]]>Utrecht University has invested in four different Life Science hubs: the Utrecht Exposome Hub, the Utrecht Platform for Organoid Technology, the Utrecht Molecular Immunology Hub and the Utrecht Advanced In Vitro Models Hub.

What role do bioinformaticians play in the ULS hubs?

These hubs bring together excellent researchers from different disciplines to work on on societal problems and scientific challenges. Bioinformatics and research groups affiliated with the Utrecht Bioinformatics Center also play an important role in these hubs, as they actively participate in the Exposome Hub and Molecular Immunology Hub. In addition, bioinformatics expertise and tooling are also in high demand to take advantage of the predictive capabilities of organoids in clinical care.

]]>Oncode is the independent institute dedicated to outsmarting cancer and impacting lives. Two of the 19 newly selected Oncode Investigators are UBC junior PI’s Jeroen de Ridder and Ruben van Boxtel. Congratulations to both!

Selected over open recruitment

Utrecht Bioinformatics Center is very honoured and proud that these two junior principal investigators have been selected over the course of two open recruitment calls. Dr Jeroen de Ridder of UMC Utrecht will work on applying machine learning methods towards predicting cancer phenotypes. Dr Ruben van Boxtel of the Hubrecht Institute investigates why children get cancer.

Cancer research

Oncode is a virtual institute that brings together excellent cancer researchers with the goal of improving patient survival and quality of life. In taking the results of fundamental research to market, Oncode enables new startups and their innovative solutions to blossom.